AMBER: please help us on partial charge calculation of PT complex using RESP

From: <>
Date: Fri, 01 Jul 2005 11:10:31 -0400

Dear Colleagues,

We are trying to conduct ab initio calculation for the partial point charges
of a PT-DNA adduct complex. The charge of PT we obtained from RESP is out of
our expectation. Since PT is a very high atomic number (78) heavy atom, we
are wondering whether or not RESP could handle it. We also would like to hear
about any advice about how to obtain the accurate partial charge for such
heavy atom in complex. We will detail our ab initio calculation procedures
and we would like you to help us identify any potential problems.

We started from available NMR solution or crystal structure and built
[Pt(NH3)2(9meGua)2]2+ (Cisplatin) using insightII in order to simplify the
system for following QM calculation. (See structure in attachment ?structure

Then we wrote our own Gaussian 03 input script to perform the QM calculation.
We first performed the minimization / geometry optimization for the structure
and then generated the molecular electrostatic potential. (See Gaussian 03
input script in attachment ?Gaussian 03 input.doc?.)

Final steps, we ran espgen from AMBER 8 package to get the .esp file and it
espgen ?i Gaussian_03_output.log ?o filename.ESP
Since AMBER or ANTECHAMBER program could not recognize PT atom and bonds bound
to PT, we prepared our own two stage RESP input files. (See RESP input scripts
in attachment ?RESP1.IN? and ?RESP2.IN?.) There was no error messages
generated and RESP completed silently. However the final charge we obtained
is unexpected. From previous work done by other group, the charge of PT in
the same complex is around +0.7 but we obtained -0.1.

As far as our understanding, in order to let RESP run, the only necessary
files are .ESP and two two-stage RESP input files. RESP does not need any
information from AMBER. Thus though AMBER or ANTECHAMBER failed to recognize
PT atom and bonds bound to PT, it should not affect RESP. So we could claim
RESP as a standalone program. However we guess within RESP program, it should
be able to recognize certain atom types, like H, C and N etc, in order to do
the right charge fitting. Thus we are wondering whether PT atom type is
defined in RESP or not because in gaff.dat file within AMBER, S (16) is the
largest atomic number atom defined.

Thank you for your help and we are looking forward to your reply soon.

Sincerely yours,

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Received on Fri Jul 01 2005 - 16:53:00 PDT
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